Hypothes.is should really try to do a better job of preventing abuse in these types of situations so writers needn't worry about providing abusers the ability to use a writer's own platform to harass them. Perhaps borrowing the NIPSA concept from Flickr for flagged annotations and/or accounts? (NIPSA is an acronym for "Not In Public Site Areas", and an admin feature of Flickr that allows their support staff to mark an account such that posts from it will not be shown in search results and other similar public views of posts.)

Prior to the WPTavern post which motivated the conversation, there was a [https://hypothes.is/blog/annotation-is-now-a-web-standard/ post written by Dan Whaley of Hypothes.is] who worked extensively within the group. This post has some interesting overview, but those interested in a fully implemented annotation platform (presumably using many of the pieces of the proposed standard) should take a quick look at [https://hypothes.is/ Hypothes.is], what it is and what it allows. Their front page has a pretty useful video introduction.

Keep in mind that some of the standard is geared specifically toward browsers and browser vendors, though WordPress could certainly implement some of the pieces from the CMS side.

Common recommendations for cell line authentication, annotation and quality control fall short addressing genetic heterogeneity. Within the Human Toxome Project, we demonstrate that there can be marked cellular and phenotypic heterogeneity in a single batch of the human breast adenocarcinoma cell line MCF-7 obtained directly from a cell bank that are invisible with the usual cell authentication by short tandem repeat (STR) markers. STR profiling just fulfills the purpose of authentication testing, which is to detect significant cross-contamination and cell line misidentification. Heterogeneity needs to be examined using additional methods. This heterogeneity can have serious consequences for reproducibility of experiments as shown by morphology, estrogenic growth dose-response, whole genome gene expression and untargeted mass-spectroscopy metabolomics for MCF-7 cells. Using Comparative Genomic Hybridization (CGH), differences were traced back to genetic heterogeneity already in the cells from the original frozen vials from the same ATCC lot, however, STR markers did not differ from ATCC reference for any sample. These findings underscore the need for additional quality assurance in Good Cell Culture Practice and cell characterization, especially using other methods such as CGH to reveal possible genomic heterogeneity and genetic drifts within cell lines.

Towards the end of using this plugin as part of an online "notebook" or commonplace book, it would be nice to have finer control over the listings of the annotations.

As an example, look at: http://boffosocko.com/2016/06/18/a-new-thermodynamics-theory-of-the-origin-of-life-quanta-magazine/
The original post was a "bookmark" to an article which was then annotated, solely by me. When embedding the annotations (in this case the shortcode included one author and one specific tag), it becomes overly redundant to repeatedly include that the annotations were by me, that they're from the same article, and including the picture multiple times. As this is likely a frequent use case for such a plug in, perhaps when the same annotator is repeated all the annotations could come under one heading and similarly if it's the same article, those could be concatenated along with just one photo as well.

This type of logic isn't too difficult given the current configuration though it may require some thought for the pending changes to add and/or functionality for multiple authors and multiple tags.

One particular hurdle may be cases where the order of annotations could potentially tell a "story" and even more so when there are multiple authors providing multiple annotations (for example when using this in a classroom setting versus a single-author notebook.)

Providing a visual indicator like # which includes a wrapped permalink URL for the particular article could allow the user to also quickly jump to that page and see the broader flow of annotations on a single page, especially in a classroom type setting where dozens of students may have made hundreds of annotations which may provide a slightly better contextual UI experience, while still allowing the (shortcoded) web page to include all of the annotations for historical purposes.

This plugin is spectacular by the way... Here are some thoughts on future development:

It would be great if the displayed text output from the shortcode included a permalink to the original annotation on Hypothesis. As a UI suggestion, perhaps you could place it after the title of the annotated page thusly:
URL WRAPPED TITLE | &lt; a href="permalinkhere">#&lt;/a>

Being able to circumscribe dates for displayed annotations could be useful, particularly in cases where one wants to highlight only a handful of annotations from a particular user with a particular tag but specific ones within certain time parameters. Additionally pages with embeds could, over time, require importing huge numbers of annotations which may not be ideal, or the context may change with significant future annotations that aren't relevant to what could be a static post that's trying to highlight just a few particular annotations. Time parameters could also prevent future possible spam on unwatched embeds with only "tag" parameters that could be targeted by bad actors.

As someone who uses <a href="http://www.boffosocko.com">my own WordPress site</a> as a research notebook/tool and commonplace book (as well as for owning all of my own data and social posts), I'm <a href="http://boffosocko.com/2016/06/17/hypothes-is-and-the-indieweb/">already loving</a> this plugin and can see some tremendous potential for improvements on both it and on the hypothes.is platform in the future.

While I've played around with other platforms like Genius.com as well, Hypothes.is seems to have a more focused approach to how I prefer to use annotations, highlights, and marginalia on the web. It also has a growing API and related suite of tools which portend more flexibility and growth for the future.